How to make timecode track in transcoded file match original

Using Compressor 4.1.3, when I make an H264 QT from a DNX36 QT, the timecode track does not replicate properly. The first frame of timecode repeats for a frame which makes every frame after that read as one frame earlier than it is in the original file.

For example, the first frame of the original file is 01:00:00:00. In the H264, the 1st and 2nd frames are 01:00:00:00, and the 3rd frame is 01:00:00:01. The 3rd frame should be 01:00:00:02.

The DNX36 is a QT Reference movie exported from Avid MC 7.0.4.1. I am reading the timecode on the QuickTimes using QuickTime Player 7.6.6. This works correctly with Mac OS 10.7.5 and Compressor 3.5.3.

The system I'm having the trouble on is Mac OS 10.9.4, Compressor 4.1.3

Any ideas on how to make the timecode track of the transcoded file match the original?

Thanks.